MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.

The bHLH (basic helix–loop–helix) transcription factors function as crucial regulators in numerous biological processes including abiotic stress responses and plant development. According to our RNA-seq analysis of tomato seedlings under salt stress, we found that, although the bHLH gene family in tomato has been studied, there are still so many tomato bHLH genes that have not been identified and named, which will hinder the later study of SlbHLHs. In total, 195 SlbHLHs that were unevenly distributed onto 12 chromosomes were identified from the tomato genome and were classified into 27 subfamilies based on their molecular features. The collinearity between SlbHLHs and interrelated orthologs from 10 plants further revealed evolutionary insights into SlbHLHs. Cis-element investigations of SlbHLHs promotors further suggested the potential roles of SlbHLHs in tomato development and stress responses. A total of 30 SlbHLHs were defined as the differentially expressed genes in response to salt stress by RNA-seq. The expression profiles of selected SlbHLHs were varyingly and markedly induced by multiple abiotic stresses and hormone treatments. These results provide valuable information to further understand the significance and intricacy of the bHLH transcription factor family, and lay a foundation for further exploring functions and possible regulatory mechanisms of SlbHLH members in abiotic stress tolerance, which will be significant for the study of tomato stress resistance and agricultural productivity.